Find sequence motif combinations according to custom specification.
The motif search itself is currently made by FIMO from MEME suite.
Given motif combination, the script will find all motifs individually with FIMO and then filter them, so their reported
combinations follows the given criteria (order, strand, distance).
The score of the combined motif satisfying given criteria is taken as a sum of the scores. The p-value for the combined
motif can be optionally computed with pytfmpval package (separate installation is needed at this moment).
- Fimo: Charles E. Grant, Timothy L. Bailey and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics 27(7):1017-1018, 2011.
- pytfmpval: Touzet, H., Varré, JS. Efficient and accurate P-value computation for Position Weight Matrices. Algorithms Mol Biol 2, 15 (2007). https://doi.org/10.1186/1748-7188-2-15